MolNFT v1 · #171533 · protein
Structure of [nifese] hydrogenase from desulfovibrio vulgaris hildenborough pressurized with oxygen gas - structure WTO2
6Z8J · Periplasmic [nifese] hydrogenase, small subunit: “Structure of [nifese] hydrogenase from desulfovibrio vulgaris hildenborough pressurized with oxygen gas…”. X-ray diffraction, 8 ligands (SF4, 6ML, FCO), 11 pockets (best druggability…
- PDB
- 6Z8J
- Type
- protein
- Length
- 1,523 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic [nifese] hydrogenase, small subunit; Periplasmic [nifese] hydrogenase, large…
- EC
- 1.12.7.2
- UniProt
- Q72AS4, Q72AS3
- Ligands
- SF4, 6ML, FCO, NI, FE2, H2S, CL, OXY
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Periplasmic [nifese] hydrogenase, small subunit (EC 1.12.7.2) | protein | 279 | 42% helix, 17% strand | Q72AS4 |
| B | Periplasmic [nifese] hydrogenase, large subunit, selenocysteine-containing (EC 1.12.7.2) | protein | 484 | 44% helix, 19% strand | Q72AS3 |
| D | Periplasmic [nifese] hydrogenase, large subunit, selenocysteine-containing (EC 1.12.7.2) | protein | 481 | 44% helix, 19% strand | Q72AS3 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C, D
- 6ML · oxygen-damaged SF4 · ligand · 2 copies · chains A, B, C, D
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains B, D
- NI · Nickel (II) ion · metal · 2 copies · chains B, D
- FE2 · Fe (II) ion · metal · 2 copies · chains B, D
- H2S · Hydrosulfuric acid · ion · 2 copies · chains B, D
- CL · Chloride ion · ion · 2 copies · chains B, D
- OXY · Oxygen molecule · ion · 2 copies · chains B, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.79 | 0.98 | 33 | empty |
| 2 | 929 | 0.78 | 0.81 | 78 | empty |
| 3 | 106 | 0.77 | 0.96 | 39 | empty |
| 4 | 227 | 0.57 | 0.79 | 33 | GOL |
| 5 | 242 | 0.57 | 0.78 | 31 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3364 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 3340 Ų buried · 53 hydrogen bonds · protein-protein
- A–D · 334 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, oxidation).
Compared structures
- 6Z8J · Structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris hildenborough pressurized… · the same entry in another collection · chain D against D, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q72AS4
- Every structure of UniProt Q72AS3
- Elsewhere: RCSB PDB 6Z8J · PDBe 6Z8J · UniProt Q72AS4 · UniProt Q72AS3
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